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Phylogenetic Placement

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Alexandros Stamatakis

Feb 2

Deadline extension - February 6 - Crete, Greece, May 2026: Mathematical and Computational Evolutionary Biology Meeting

Dear Users of our Tools, The submission deadline for the 2026 Mathematical and Computational

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Deadline extension - February 6 - Crete, Greece, May 2026: Mathematical and Computational Evolutionary Biology Meeting

Dear Users of our Tools, The submission deadline for the 2026 Mathematical and Computational

Feb 2

Alexandros Stamatakis2

Jan 26

Deadline approaching (Jan 31st) Crete, Greece, May 2026: Mathematical and Computational Evolutionary Biology Meeting

Dear Users of our Tools, The abstract submission deadline (Jan 31st) for the 2026 Mathematical and

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Deadline approaching (Jan 31st) Crete, Greece, May 2026: Mathematical and Computational Evolutionary Biology Meeting

Dear Users of our Tools, The abstract submission deadline (Jan 31st) for the 2026 Mathematical and

Jan 26

Alexandros Stamatakis

Jan 6

Submission Deadline Jan 31st: 2026 Mathematical and Computational Evolutionary Biology Meeting in Crete

Dear Users of our Tools, The submission deadline (Jan 31st) for the 2026 Mathematical and

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Submission Deadline Jan 31st: 2026 Mathematical and Computational Evolutionary Biology Meeting in Crete

Dear Users of our Tools, The submission deadline (Jan 31st) for the 2026 Mathematical and

Jan 6

Alexandros Stamatakis

12/15/25

Permanent Research Group Leader Position, Crete, Greece: Biodiversity Computing

Dear All, There is a permanent research group leader position available in Crete, Greece. The

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Permanent Research Group Leader Position, Crete, Greece: Biodiversity Computing

Dear All, There is a permanent research group leader position available in Crete, Greece. The

12/15/25

Alexandros Stamatakis

12/5/25

May 2026 Crete, Greece: Mathematical and Computational Evolutionary Biology Meeting

Dear Users of our Tools, Please consider joining us in Crete in May 2026 for the annual instance of

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May 2026 Crete, Greece: Mathematical and Computational Evolutionary Biology Meeting

Dear Users of our Tools, Please consider joining us in Crete in May 2026 for the annual instance of

12/5/25

Alexandros Stamatakis

11/3/25

Crete, Greece, May 2026: Mathematical and Computational Evolutionary Biology Meeting

Dear Users of our Tools, Please consider joining us in Crete in May 2026 for the annual instance of

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Crete, Greece, May 2026: Mathematical and Computational Evolutionary Biology Meeting

Dear Users of our Tools, Please consider joining us in Crete in May 2026 for the annual instance of

11/3/25

Alexandros Stamatakis

11/3/25

Dear Users of our Tools, Please consider joining us in Crete in May 2026 for the annual instance of

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Dear Users of our Tools, Please consider joining us in Crete in May 2026 for the annual instance of

11/3/25

Alexandros Stamatakis

10/13/25

Register by Oct 17: Machine Learning for Evolutionary Genomics Data Conference - French Alps

Dear Users of our SW tools, October 17 is your last chance to register for the 2nd conference on

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Register by Oct 17: Machine Learning for Evolutionary Genomics Data Conference - French Alps

Dear Users of our SW tools, October 17 is your last chance to register for the 2nd conference on

10/13/25

franco magurno, Lucas Czech3

9/12/25

Internal node truncated taxonomic affiliation

More details about the analysis: gappa edit accumulate --jplace-path epa_result.jplace --threshold

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Internal node truncated taxonomic affiliation

More details about the analysis: gappa edit accumulate --jplace-path epa_result.jplace --threshold

9/12/25

Alexandros Stamatakis

9/1/25

Machine Learning for Evolutionary Genomics (Legend2025) abstract submission deadline: September 2022

Dear Users of our SW tools, Do you want to spend time in the French Alps and talk about Machine

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Machine Learning for Evolutionary Genomics (Legend2025) abstract submission deadline: September 2022

Dear Users of our SW tools, Do you want to spend time in the French Alps and talk about Machine

9/1/25

Alexandros Stamatakis

6/18/25

2nd Conference on Machine Learning for Evolutionary Genomics - French Alps

Dear Users of our Software Tools, Do you fancy spending some days in the French Alps in December and

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2nd Conference on Machine Learning for Evolutionary Genomics - French Alps

Dear Users of our Software Tools, Do you fancy spending some days in the French Alps in December and

6/18/25

Alexandros Stamatakis

3/19/25

raxtax: a novel tool for taxonomic classification

Dear Users Check out raxtax, our new open-source tool for taxonomic classification of barcoding

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raxtax: a novel tool for taxonomic classification

Dear Users Check out raxtax, our new open-source tool for taxonomic classification of barcoding

3/19/25

Alexandros Stamatakis

2/24/25

LEGEND conference on Machine Learning for Evolutionary Genomics Data - French Alps - Dec 8-12 2025

Dear Users of our tools, The second edition of our LEGEND conference on Machine Learning for

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LEGEND conference on Machine Learning for Evolutionary Genomics Data - French Alps - Dec 8-12 2025

Dear Users of our tools, The second edition of our LEGEND conference on Machine Learning for

2/24/25

Francesco Ravaioli, Lucas Czech3

12/31/24

Issues with Picrust2 Installation on M2 Macbook

Hi Francesco, all right, thanks. Let us know if there is any other trouble :-) Cheers and a Happy New

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Issues with Picrust2 Installation on M2 Macbook

Hi Francesco, all right, thanks. Let us know if there is any other trouble :-) Cheers and a Happy New

12/31/24

Alexandros Stamatakis

10/21/24

Applications for 2025 computational molecular evolution summer school close in 10 days

Dear Users of our software tools, Applications are still open for the 2025 school on computational

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Applications for 2025 computational molecular evolution summer school close in 10 days

Dear Users of our software tools, Applications are still open for the 2025 school on computational

10/21/24

Soledad De Esteban Trivigno

10/9/24

Live Online Course: Introduction to phylogenomics, November 4-18, 2024

Dear colleagues, I am excited to let you know that we have a new edition of Transmitting Science

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Live Online Course: Introduction to phylogenomics, November 4-18, 2024

Dear colleagues, I am excited to let you know that we have a new edition of Transmitting Science

10/9/24

Alexandros Stamatakis

10/8/24

Applications for 2025 computational molecular evolution summer school close in 3 weeks

Dear Users of our software tools, Applications are still open for the 2025 school on computational

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Applications for 2025 computational molecular evolution summer school close in 3 weeks

Dear Users of our software tools, Applications are still open for the 2025 school on computational

10/8/24

Alexandros Stamatakis

9/17/24

Registrations for 2025 computational molecular evolution summer school are open

Dear Users of our software tools, Registrations are open for the 2025 school on computational

unread,

Registrations for 2025 computational molecular evolution summer school are open

Dear Users of our software tools, Registrations are open for the 2025 school on computational

9/17/24

Alexandros Stamatakis

8/7/24

Registrations for 2025 computational molecular evolution summer school are open

Dear Users of our software tools, Registrations are open for the 2025 school on computational

unread,

Registrations for 2025 computational molecular evolution summer school are open

Dear Users of our software tools, Registrations are open for the 2025 school on computational

8/7/24

Thanu Chami, Alexandros Stamatakis2

8/5/24

Issue with multi-gene partition Model File in EPA-ng

Dear Fernando, I would proceed as follows: As you are trying to place COI sequences in a fixed tree

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Issue with multi-gene partition Model File in EPA-ng

Dear Fernando, I would proceed as follows: As you are trying to place COI sequences in a fixed tree

8/5/24

Kenta Renard, Lucas Czech5

7/3/24

Gappa "Invalid Color Normalization with min >= max" error

Hi Kenta, thanks for sharing the files. Indeed, as suspected, the jplace file contains the values

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Gappa "Invalid Color Normalization with min >= max" error

Hi Kenta, thanks for sharing the files. Indeed, as suspected, the jplace file contains the values

7/3/24

Kenta Renard, Alexandros Stamatakis4

3/15/24

EPA-NG taxa in tree not found in reference MSA

Dear Kenta, I assume the problem is the discrepancy between FASTA and tree file names, eg you have in

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EPA-NG taxa in tree not found in reference MSA

Dear Kenta, I assume the problem is the discrepancy between FASTA and tree file names, eg you have in

3/15/24

3/4/24

Zero-length branches bug

Hello, My question relates to this open issue on epa-ng here: https://github.com/pierrebarbera/epa-ng

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Zero-length branches bug

Hello, My question relates to this open issue on epa-ng here: https://github.com/pierrebarbera/epa-ng

3/4/24

Alexandros Stamatakis

1/16/24

Crete May 2024 - Machine Learning for Evolutionary Genomics Data

Dear Users of our Software, Sorry for bothering you with some event advertisement again via this list

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Crete May 2024 - Machine Learning for Evolutionary Genomics Data

Dear Users of our Software, Sorry for bothering you with some event advertisement again via this list

1/16/24

Alexandros Stamatakis

11/15/23

Two weeks remaining to apply for 2024 Summer School on Computational Molecular Evolution

Dear Users of our software tools, The deadline for applications to our 14th summer school on

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Two weeks remaining to apply for 2024 Summer School on Computational Molecular Evolution

Dear Users of our software tools, The deadline for applications to our 14th summer school on

11/15/23

Alexandros Stamatakis

10/26/23

Applications for 2024 Summer School on Computational Molecular Evolution are open

Dear Users of our software tools, The applications for our 14th summer school on COmputational

unread,

Applications for 2024 Summer School on Computational Molecular Evolution are open

Dear Users of our software tools, The applications for our 14th summer school on COmputational

10/26/23

Narfusala, Alexandros Stamatakis2

8/28/23

EPA-ng use case?

Dear Lesly, That is correct, there has been one attempt to do this with metagenomic data: https://www

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EPA-ng use case?

Dear Lesly, That is correct, there has been one attempt to do this with metagenomic data: https://www

8/28/23

Alexandros Stamatakis

7/11/23

One PostDoc Positions in my new research group in Crete

Dear Users of our Software, Please accept my apologies that I am slightly misusing our software

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One PostDoc Positions in my new research group in Crete

Dear Users of our Software, Please accept my apologies that I am slightly misusing our software

7/11/23

Sigmund Jensen, … Lucas Czech7

6/7/23

Hi Lucas, yes, it means things work now. I just have to remove or rename that file 'epa_info.log

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Hi Lucas, yes, it means things work now. I just have to remove or rename that file 'epa_info.log

6/7/23

Otávio Lovison, … Lucas Czech5

6/6/23

Outliers detection and treatment

Very interesting! About chimeras: I will perform some tests.. About taxonomic assignment: I was

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Outliers detection and treatment

Very interesting! About chimeras: I will perform some tests.. About taxonomic assignment: I was

6/6/23

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